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Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?

Bioinformatics Asked on September 5, 2021

This is my first post here. I can think of no way of giving an easily reproducible example, as per the stack ethos. SO apologies in advance and any feedback on question format appreciated.

I have called samtools mpileup (Version: 1.9 (using htslib 1.9)) on some oxford nanopore data (mapped to GRCh38).

I am seeing some instances like below (grouped with pythons Counter), here reference is T at this position:

 Counter({',': 34, '.': 33, 'c': 9, 'g': 6, 'a': 4, 't': 2, '-:ACTC': 1, '-:ACTCGG': 1, '-:5': 1, '$': 1, '*': 1})

Why is ‘t’: 2′ in there?

flags used: -A -B -Q 1 -R -x

One Answer

Why is 't': 2' in there?

How else do you think the pileup should show you that two reads (in the reverse direction) have a T in that position?

Answered by swbarnes2 on September 5, 2021

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